Creationists often say that
all
mutations are harmful and deleterious, and degrade the genome. They
say that mutations can only scramble the information that's there,
and that
mutations cannot
produce new "information." This
page shows why they are wrong.

Last Update: November 5,
2004

Wondering about Answers in Genesis and their "refutation" of
the Nylon Bug as due to plasmids? - Click here
for an update!

How about Answers in Genesis and the TJ Vol. 17 #3 article
"The adaptation of bacteria to feeding on nylon waste" by Don
Batten? Click here for an update!

Lee Spetner, author of Not By Chance, has taken on the Nylon Bug.
Click here for an update!

The Nylon Bug

My favorite example of a mutation producing new information
involves a Japanese bacterium that suffered a frame
shift mutation that just happened to allow it to metabolize
nylon waste. The new enzymes are very inefficient (having only 2% of
the efficiency of the regular enzymes), but do afford the bacteria a
whole new ecological niche. They don't work at all on the bacterium's
original food - carbohydrates. And this type of mutation has even
happened more than once!

So, what is a frame shift mutation?

It happens when a chunk of genetic code (remember those
AGTCTAGATCGTATAGC... DNA sequences from Jurassic
Park?) is shifted by one or more nucleotides. In DNA,
each triplet of nucleotides codes for one amino acid, and each such
triplet is called a codon. So, the amino acid Arginine
(symbol Arg) is coded by the DNA nucleotide sequence CGT, and
also by codons CGA, CGC,CGG, AGA, AGG. Likewise, the amino acid
Glutamic Acid (symbol Glu) is coded by the DNA nucleotide
sequence GAA, and also by the sequence GAG. There are four types of
nucleic acids, which naturally bond in one of two pairs:
Thymine/Adenine, and Cytosine/Guanine (T/A and G/C).
A thymine (T) on one strand of DNA will bind to an
adenine (A) on the paired strand, and so on. There would be 64
different possible amino acids with a three-nucleotide codon
(43=64), but several of these are redundant, as shown in
the lists above for amino acids Arginine and Glutamic Acid. In
biological organisms, there are just 20 different amino acids.
Various DNA triplets code for these amino acids, and strings of
amino acids form proteins - molecules (such as enzymes)
that really do something specific, such as metabolize sugars.

A Frame Shift is a radical mutation in which a single
nucleotide is inserted or deleted, causing a shift in the triplets
coded by the DNA strand. It's fairly technical, so I'll present
what a Frame Shift is by analogy with a different Digital Code, that
being the ASCII code used in computers to convert numbers from 0
to 255 into symbols or characters. For example, the ASCII code
for the letter "A" is 65, which in binary converts to 64+1, or
26 + 1, written thus: 01000000 + 00000001 =
01000001. For this analogy, we'll just be using the first 128
characters, and so we can use just 7 digits: thus, an
"A" then has the 7-digit code 1000001. A lower case "a" is
32 higher than a capital A (which leaves room for 26 letters and
a few extra characters), and is thus written 1100001 in 7-digit
binary notation (=64+32+1 = 97 in decimal). A "b" is
written 1100010 in 7-digit binary notation (=64+32+2 = 98). Likewise,
a "d" is written 1100100 in 7-digit binary notation (=64+32+4 =
100), and an "e" is written 1100101 in 7-digit binary
notation (=64+32+4+1 = 101).

What has all this to do with Frame Shifts, you ask? In this
analogy, actual biological proteins or enzymes (strings of amino
acids) correspond to words or phrases (strings of
ASCII characters). Individual amino acids (such as Arginine) are
analagous to individual ASCII characters (such as the letter
"A"). Finally, the DNA nucleotides A, T, C and G correspond
to the binary digits 0 and 1.

So, let us string together several letters to make a "digital"
word. The ASCII digital code for the word "bed" is made by
stringing together the 7-digit codes for b (1100010), e (1100101),
and d (1100100) to make one long
code: 110001011001011100100.

The image below shows what happens when we apply a Frame Shift to
the digital code for bed. Here, we shift the "reading frame" by
one digit to the left, which requires that we add one extra digit as
a prefix. Here, the prefix I chose was the digit 1.

The Frame Shift is not a mild mutation. It is HUGE. We
still have a 3-letter string, but each letter is different. Shifting
the reading frame one digit gives us three
NEW characters: q:(1110001), 2 (0110010), and r
(1110010).

This particular Frame Shift scrambles the perfectly fine word
"bed" into the unintelligible, meaningless word "q2r." In this
case, the Frame Shift is not only a drastic mutation, but has
completely altered the meaning of the word "bed." In this case,
at least, information has been "lost"or "degraded," just as
creationists say will happen ALL THE TIME -
EVERY TIME.

And that's where they are wrong. While most
Frame-Shift mutations do indeed scramble meanings and degrade
information, not all of them do so.

Here's an example of a frame shift creating
information: here, the word "gas" is coded as
g(1100111) + a (1100001) + s (1110011). When we
apply a Left Frame Shift to the long code for "gas," we do
NOT end up with a meaningless phrase such as
"q2r." In THIS case, we end up with a new, meaningful
word: spy.

Similarly, the word "jib," when right-frame-shifted, is
mutated into the new word "USE."

As a final example, the word "ICE," when left-frame-shifted, is
mutated into the new word "dab."

Certainly, MOST frame shifts will destroy information.
BUT NOT ALL - and that is where creationists have it
wrong. I have shown three examples where such "Frame
Shifts" indeed create new information. After all, in the proper
context, the words "spy," "USE," and "dab" actually
mean something. Since their meanings are totally unrelated to the
original meanings, it is obvious that, at least in this case, the
Frame Shift mutation process has created
new information.
It's important to note that context really means something as
regards interpretation of these words. For example, if the word
"luz" was generated, that would mean nothing in English,
but it means "light" in Spanish. Without a common language and
culture, words won't mean anything! It's different with DNA, because
the "context" in which DNA strands are interpreted is the
world of chemical reactions. The "meaning" of novel strands of
DNA lies in how these strands are transcribed, what the new
proteins look like, and (most importantly!) how the proteins
react with other molecules, perhaps even affecting the organism's
lifestyle.

Now, let's get back to Biology, and the case of the bacterium
which has evolved the capability of ingesting nylon waste (see
Kinoshita et. al.). This case is most interesting. Nylon
didn't exist before 1935, and neither did this organism. Detailed
examination of the DNA sequences of the original bacterium and of the
nylon-ingesting version show identical versions in the gene for a key
metabolic enzyme, with only one difference in over 400 nucleotides.
However, this single microevolutionary addition of a single thymine
('T') nucleotide caused the new bacterium's enzyme to be composed of
a completely novel sequence of amino acids, via the
mechanism of frame shifting. The new enzyme is 50 times less
efficient than its precursor, as would be expected for a new
structure which has not had time to be polished by natural selection.
However, this inefficiency would certainly not be expected in the
work of an intelligent designer. The genetic mutation that produced
this particular irreducibly-complex enzyme probably occurred
countless times in the past, and probably was always lethal, until
the environment changed, and nylon was introduced.

The image below shows just a part of the 400+-long nucleotide
string for the key enzyme (see the Susumu Ohno
paper). The original ("old") enzyme's amino acid sequence
appears on top, and the frame-shifted ("new") sequence on
bottom. The DNA nucleotides appear in the middle for both the
old species and the new (one T inserted). Over this small
portion of the enzyme, the old DNA coded for the amino acids
Arginine, Glutamic Acid, Arginine, Threonine, Phenylalanine,
Histidine, Arginine and Proline.

But the NEW DNA strand, which includes one extra
T nucleotide, is shifted, and the new string of amino acids is
completely changed. The addition of the thymine nucleotide produces a
new Methionine amino acid, which, like the conductor tapping his
baton, indicates the Start of a new Protein. This is followed by
other new amino acids because of the frame shift: Asparagine,
Alanine, Arginine, Serine, Threonine, Glycine and Glutamine. The
new string of amino acids - the new protein - is
completely different from the original.

While most frame shifts of such a key enzyme would destroy the
enzyme, resulting in immediate death of the organism, this particular
protein happened to react with nylon oligomers. And so it was that a
drastic mutation suddenly gave an ordinary sugar-eating bacterium the
unusual ability to digest nylon, which just happened to be present in
abundance in the little waste pond behind a Japanese factory. The
Japanese scientists who discovered strange bacterial mats growing in
their scum ponds became very interested in this new ability, and
finally found it was all due to a single Frame Shift mutation. The
new enzyme is not active on common substrates - the bacteria's old
"food" - and plenty were checked. Whether or not these bacteria
retain enzymes to digest their former food source, the fact is that
the former food source became much less important because of the
new-found ability to ingest food from a novel source - nylon
waste.

The creationist argument that all mutations must destroy
information is clearly wrong. In this case, a mutation has clearly
produced new information. That is, unless you want to quibble that
the detailed three-dimensional structure and composition of a protein
that reacts specifically to nylon is not "information."

Creationists usually counter this example by claiming that the
bacterium is, after all, "still a bacterium." It didn't
mutate into a whale or a dinosaur. But that's changing the subject.
The subject of this essay is "Can Mutations Create New
Information."

Therefore, this organism could not have existed before 1935.
Where did it come from? Why, it
evolved.

Thwaites noted that "All of this
demonstrates that Yockey (1977a and b), Hoyle and Wickramasinghe
(1981), the creationists (Gish, 1976), and others who should know
better are dead wrong about the near-zero probability of new
enzyme formation."

Key Quote: "There are two possible reasons for
an enzyme to be active on an unnatural substrate: one is that an
unnatural compound could be decomposed by an enzyme if it were an
analogue of that enzyme's physiological substrate, and the other
is that an unnatural substrate could be decomposed by a newly
evolved enzyme. The data obtained in this study show that
6-aminohexanoic-acid-oligomer hydrolase has no activity on any
physiological substrates, including the linear and cyclic amides
and peptides tested..."

"... Finally, Mr Cerutti is out of date about this new
nylon digesting ability allegedly from a frame shift.
New evidence shows that the ability was due
to plasmids [e.g. K. Kato, et al.,
A plasmid encoding enzymes for nylon oligomer degradation:
Nucleotide sequence analysis of pOAD2, Microbiology
(Reading) 141(10):25852590, 1995. In
fact, more than one species of bacteria have the ability, residing
on plasmids. This suggests that the information probably already
existed, and was just passed between different types of bacteria.
..."

Sorry, AiG, but just because something is on a plasmid doesn't
mean it's always been there! In fact, the plasmid involved in
this case is very well known and characterized. Scientists have
studied both the original (pre-mutation) plasmid and the novel
(post-mutation) plasmid, in great detail. It turns out that the novel
plasmid's mutated DNA for production of nylonase is almost
identical to a non-coding repetitive DNA sequence on the original
plasmid; the difference is the single nucleotide that triggered the
Frame Shift. This mutation did not exist 60 years ago. If this gene
was always there, whether in a plasmid or not, we can reasonably
wonder why a bacteria would have a gene for hydrolysing an artificial
polymer that did not exist until just a few decades ago; and why, in
the absence of such a substrate, was the gene not mutated to
uselessness over the millenia?

Was the plasmid slipped in from another
bacterium? NO!! The plasmid in question, pOAD2, is
just one of three plasmids that are harbored by the bacterium under
investigation here, Flavobacterium Sp. K172. Here are some
citations to back this up:

"Analysis of the published base sequence residing
in the pOAD2 plasmid of
Flavobacterium sp. K172 indicated that the
392-amino acid-residue-long bacterial enzyme 6-aminohexanoic acid
linear oligomer hydrolase involved in degradation of nylon
oligomers is specified by an alternative open reading frame of the
preexisted coding sequence
that originally specified a
472-residue-long arginine-rich
protein."

It's interesting to note that the precise plasmid of
Flavobacterium sp. K172, namely pOAD2, was cited by Susumu
Ohno fully eleven years before the publication of the
"new evidence" that AiG claims " shows that the
ability was due to plasmids..."

The Bottom Line: Just because this mutation wasn't confined
to a cell's main chromosomes does not mean it didn't happen. (A
plasmid is defined
as a replicon
- a replicating piece of DNA - that is inherited in an
extrachromosomal state.) This case still provides an excellent
example of a New Protein that evolved without the assistance of an
Intelligent Designer.

(My thanks to Ian Musgrave and Ian Ferguson for useful discussions
on this topic).

UPDATE: Don
Batten of "Answers In Genesis" writes on "The adaptation of bacteria
to feeding on nylon waste" in the Technical Journal, Vol. 17, Issue 3
(December 2003)

"However, there are good reasons to doubt the claim
that this is an example of random mutations and natural selection
generating new enzymes, quite aside from the extreme improbability
of such coming about by chance. ..."

"It's interesting, first of all, that the URL you
pointed to picked the "nylon bug" as an example of a random
mutation yielding a gain of information. (The short answer is, the
mutation does yield an increase of
information, but was it random?) . ... Let me
point out two important facts that the URL
[www.nmsr.org/nylon.htm] ignores. First, there are two
altered enzymes, not just one. Both these enzymes are needed to
metabolize the 6-aminohexanoic-acid-cyclic-dimer (6-AHA CD) found
in the waste water of the nylon factory. Neither of these enzymes
alone is effective. Both are needed. The first enzyme, which I
shall call enzyme 1, is 6-aminohexanoic-acid-cyclic-dimer
hydrolase (6-AHA CDH) and catalyzes the conversion of 6-AHA CD to
6-aminohexanoic-acid-oligomer (6-AHA LO). The second enzyme, which
I shall call enzyme 2, is (6-aminohexanoic-acid-oligomer hydrolase
(6-AHA LOH) and catalyzes the conversion of 6-AHA LO to
6-amino-hexanoic acid [Kinoshita et al. 1981]. Only enzyme
2 is the product of a frame shift. Enzyme 1, whose DNA sequence I
have not seen, is probably the product of only point mutations.
[Okada et al. 1983, Ohno 1984]

Second, enzyme 2 is not just the product of a frame shift,
it is also the product of 140 point mutations. Many of these
mutations are silent, but many are not. 47 amino acids out of 392
of the enzyme have been changed.

It seems to me that many of these altered amino acids are
essential to the catalytic effect of the enzyme. How many, I don't
know. In my above cited letter to Jim, I calculated the
probability of getting multiple random mutations in the 30 years
it took to evolve these enzymes. If the evolution of this enzyme
had to rely on random point mutations, it could have never
evolved. Thus, if only 6 of these 47 mutations were essential for
the evolution, the probability of achieving it in 30 years is
about 3 x 10 -35. So, if the evolution could not be
random, then it would have to be nonrandom, and as I have
suggested in my book, they would be triggered by the environment.
That is, the capability is built into the bacterium and the
environment triggers the mutations.

I have ignored the evolution of enzyme 1, and the random
evolution of that enzyme makes for an even less probable
event.

Now, why should there be a built-in capability to metabolize
nylon, which did not exist until 1937 or so? The answer is there
shouldn't be. But there could have been a built-in capability to
metabolize some other substrate. Kinoshita et al. (1981) tested
enzyme 2 against 50 possible substrates and found no activity, but
that does not mean that it doesn't have activity on some substrate
not tested. The activity of enzyme 2 was small, but enabled the
bacteria to metabolize the nylon waste. "

DISCUSSION

For starters, it appears that Spetner is suggesting that the
mutations involved in the formation of nylonase enzymes were somehow
caused by the environment, or made more likely because of the
environment. But to make this case hold, Spetner should demonstrate
that the 'right' mutations happened much more often than 'wrong'
mutations. He's done nothing of the sort.

Additionally, Spetner's calculation of probability appears to
assume that all the point mutations must occur
simultaneously, which would give numbers like he specifies. However,
he has produced no biological evidence that this supposed
simultaneity is necessary.

Here are two key articles that counter Spetner's claims.

"Single-gene speciation by leftright reversal"How many genetic mutations are required for the formation of a
new species? Is it 37? 140? 500?
This article, by Rei Ueshima and Takahiro Asami, appeared in Nature
425, 679, 16 October 2003, and shows that a mutation in ONE gene
in a snail was enough to produce sexual isolation, and thus a new
species. The gene controls the handedness of the snail's shell, and
right-handed forms simply cannot mate with left-handed ones. When
both right and left-handed specimens of the snail Euhadra were
found, DNA analyses were performed, and it was found that a
mutation in a single gene was responsible for the speciation
event.
(abstract,
PDF of
paper -
WARNING! GRAPHIC PICTURES OF SNAIL SEX)

"Functional proteins from a random-sequence library"
Spetner implies that the particular forms of nylonase studied must
have a precisely specified sequence for the entire enzyme. This
assumption is what drives his low-probability estimates, like the
figure of 3 x 10 -35 cited above. However, this paper by
Keefe and Szostak discusses a study of the likelihood of any
randomly-formed protein having significant biological activity. They
studied "a library of 6 x 1012 proteins each containing
80 contiguous random amino acids," and then "selected
functional proteins by enriching for those that bind to ATP."
Their conclusion: "...we suggest that functional proteins are
sufficiently common in protein sequence space (roughly 1 in
1011) that they may be discovered by entirely stochastic
means, such as presumably operated when proteins were first used by
living organisms. However, this frequency is still low enough to
emphasize the magnitude of the problem faced by those attempting de
novo protein design." In other words, the formation of functional
proteins is orders of magnitude more likely than Spetner's model
suggests.PubMed

Spetner basically ignores the implications of the Keefe and
Szostak paper discussed above, and claims that

"...the debate here is whether random mutations in the
nylon bug generated the information that permitted it to
metabolize the nylon waste or was there something nonrandom about
it. By the latter I mean that either the correct mutations were
induced by the environment or else the new adaptation was already
built into the organism so that random mutations that would be
likely to occur within the population could trigger the change.

I am arguing that the above type of scenario could have
occurred to account for the nylon-bug phenomenon, and he wants to
argue that it could not have occurred that way and the only
explanation is that random mutation can often lead to adaptation
without any built-in preparation. Since these are the two sides of
the argument, it seems unjust that he should require me to prove
that the 'right' mutations (i.e. those induced by the environment)
occur more often than those that dont. On the contrary. He
should have to prove that they do not occur more often. "

Spetner admits that "the mutation does yield
an increase of information," but says this
isn't a good example of evolution because the mutations involved may
have been non-random, e.g. directed. So
it all boils down to: Are Mutations Random?

It's time for Biology 101, folks - specifically, for the Evolution
101 course from UC Berkeley's dynamic "Understanding
Evolution" website. If you follow the thread to Mechanisms,
then Genetic Variation, and finally Mutations, you'll see a page
titled "Mutations
are Random." This page says, simply, that

Experimental data do not support directed
mutation.

If you expose bacteria to an antibiotic, you will likely
observe an increased prevalence of antibiotic resistance. In 1952,
Esther and Joshua Lederberg determined that these mutations do not
happen because of exposure to the antibiotic. They showed that
bacteria with a mutation for resistance existed in the population
even before the population was exposed to the antibioticand
that exposure to the antibiotic did not cause new resistant
mutants to appear.

No known mechanism supports directed
mutation.

Imagine what would have to happen in order for a mutation to
be directed by the environment. Somehow, information
about the chemicals in the lice shampoo would have to be conveyed
to the DNA or cellular machinery. Then, something would have to
select the appropriate changes to make in the DNA and make them.
There are no known mechanisms that could do thisand
its hard to even imagine a mechanism that could do this.
Recall that science can only use natural explanations for natural
phenomena.